Chuck vs The Sins of the Father
by SteadfastWestie
Summary: For years, Chuck has lived a life where he has had little to no control over his own choices. When Agent Sarah Walker and Major John Casey enter his life, he hopes that he has found a way to escape the cage that has had him trapped for so long.


It's probably a stupid idea, but I thought I'd just get it down and see what anyone else thinks. This is a seami-AU chapter. As I progress into it, it might get further AU.

Please forgive the sudden change of title. I hated the original, but for days after I began writing it, I just couldn't come up with a better one. And then it had to come to me _after_ I posted the first chapter. Figures.

Disclaimer: Don't own Chuck.

_Chuck vs. The Sins of the Father_

**Chapter 1  
**

_**15 November 1993**_

He quietly sneaked into the office so as not to disturb his father as he worked. The room was almost completely dark, save for the silvery glow from the three computer screens that sat on a long table at one wall. The table was a mess of wires, keyboards, files, and papers that lay scattered about, as well as junk food wrappers and at least half a dozen stained and empty coffee cups. The mess – or controlled chaos, his dad might counter – was an obvious sign that he had spent a lot of sleepless nights working there.

Chuck Bartowski took in the view in front of him with a wry grin.

The grin lasted only a moment before it faded away. He really hated to interrupt his father's work, especially when he was in "the zone," but his mother was a little more on edge than usual and threatened to cause major destruction to her husband's workstation if he missed dinner with the family again.

He remembered when she used to make jokes to that effect – once upon a time. However, nowadays, he had the feeling that she might seriously do it if she became ticked off enough. Lately, it seemed like there was a storm building up inside of his mother, rumbling beneath the surface, awaiting the time when it was set loose. Even he, a young man who could accurately be considered quite naive and unobservant of the subtlety of human emotion, could see it. It scared him to death that he couldn't predict what she was going to do next. No doubt, it would be bad.

"Dad?" he called out softly, lightly tapping on the door. "Mom says that dinner's ready. I don't think it would be a very good idea to make her angry this time." He paused when there was no answer. After a moment, Chuck stepped inside the room and questioned, "Dad? Are you coming to dinner?"

Again, there was no response and he moved deeper into the room. He approached the chair, bending around in order to get a good look at his father's profile. When he saw that he had fallen asleep in the middle of his work, Chuck smiled and shook his head fondly.

This wasn't the first time Ellie or he had found him in this state. It was a common sight which often occurred when Stephen felt that he was on the verge of a breakthrough to a particularly troubling dilemma. He would end up pulling all nighters until he came up with the inevitable epiphany.

Not for the first time since Stephen had started the project a few months ago, Chuck was very tempted to try and discover what his father was working on without having him catch on. This current project of his was especially intriguing to Chuck, particularly because Stephen was being more secretive about it than any of his other projects previously.

In many ways, Stephen Bartowski was an open book, with his emotions and thoughts written on his face for the world to see. In others, especially when it came to his work, he was a little more closed off. Sometimes Chuck could coax him into letting him gain a peek. It's not like he couldn't keep what he saw a secret. Who would even think to try to steal computer industry secrets from a 13 year old?

This project was different. In the four months since Stephen started working on it, he revealed not even a hint to his son.

Chuck hesitated a brief moment, but began reaching over to one of the mouses. Just one peak wouldn't hurt. His dad would never know. He moved it slightly across the pad and his breath caught in his throat as the motion of the mouse caused a reaction from the computer.

Image after image began flickering across the screen and Chuck's eyes were drawn to them, paralyzing him and leaving him with no choice but to keep his attention on the screen. It felt as though the images were coming straight at him like a 3-D film and leaping one by one into his head. An uncomfortable pressure started to build and build and build until there was nothing in his world but the images and the discomfort.

After what could have been years, Chuck thought he could hear his father curse, but the sound was muffled, like he was hearing it while his head was submerged under water. He was drowning. He would certainly die.

Then, it all stopped. The images stopped and the pressure eased. The real world was rushing back to him. He could feel the coolness of the air conditioned room. Could hear his father speaking more clearly. Could see better the light from the now empty computer screen. Yet, he still could not move. He didn't realize it, but he was falling backwards, back as stiff as a board, the floor rushing to meet him. Chuck did not feel the impact, because he was unconscious before he hit the floor.

Slowly, he began to regain consciousness and could hear both his father's and his mother's voices, arguing quietly in the distance. He still could not move, but it was more because of the exhausted heaviness of his limbs than the same kind of paralyzing grip the images had on his body. The sound of his parents' voices kept on fading in and out, allowing him to only catch bits and pieces of what they were saying.

"You should never..."

"...no choice but to..."

"...bring them here."

"I'm sorry, Faye!"

"How many times to you have to say you're sorry bef...?"

"The important thing right now is Chuck."

"Chuck? Chuck? Wake up, Sweetie. It's Mom! I need you to wake up, honey. Stephen, we need to take him to the hospital!"

"No! We can't!"

"You should have thought of that before you brought something this dangerous home. Why couldn't you leave all of this at the lab? I should have followed my instinct and took a bat to your precious computers!"

Chuck was coming closer and closer to complete consciousness and everything that entailed. The increasing loudness of their argument was grating on him and he had to do something to get them to stop. He fought to open his eyes, which took a herculean effort.

"Mom? Dad? What happened?" he inquired when he was finally able to open his eyes and the rest of his body followed suit. He blinked up at them. His head was killing him and the light of the now completely lit room was not doing him any favors.

His mother saw him grimace in pain and quickly turned off the light. She returned to Chuck with a worried and scared expression as she looked him over, trying to assess any damage. He leaned into her touch slightly when she stroked his head. Not that she never showed any affection toward her children, but it had been a long time since she had reached out to him with such a loving gesture since the days when she tended to his aches and pains when he was a small child. It had a soothing affect.

"Sweetheart, how are you feeling?"

"Tired," he mumbled. "Head hurts."

"Don't fall asleep, baby," she insisted, leaning over him and using her hands to turn his face to force him to look at her. "I need you to try to stay awake. We're taking you to the hospital, okay?"

"Faye..." Stephen started to say, but was swiftly cut off before he could protest further.

"Hospital, Stephen," she sternly commanded, voice hard, her head whipping around to glare at her husband. To his credit, he gave in immediately, looking suitably chastened and very unhappy.

Chuck didn't remember much about his trip to the hospital that night. It wasn't until the next day – after they had him stay overnight under observation – that he started having any true memory. And that was mostly because it was in the morning that everything changed for him, setting off a chain of events that despite his father's protests, he would suffer through guilt about for the rest of his life.

_**24 September 2007**_

Chuck saw her before she caught sight of him. It was pitiful just how easy it now was for him to spot members of a surveillance team. Over the years, he had found that spooks and ghouls prided themselves on blending into their surroundings and remaining inconspicuous in a crowd.

For the most part, they succeeded. But if a person knew what they were looking for, there were always subtle signs to be spotted. Eyes that were always far more alert and observant of their surroundings than the typical civilian making his way through life. Shoulders that held a slight tension reminiscent of a tiger stalking her prey, ready to leap into action in a single, smooth moment.

There were a hundred little things that most people would miss because they were ignorant of the need. His own ignorance ended the night he had gone into his father's study while he cat napped and sneaked a peak at his government computer project, exposing Chuck to the harsh realities of the secret war fought between the world's intelligence community and its enemies.

He stamped down the bitterness that rose in his throat as he passed the 'Spook' on his way to work at the Burbank Buy More.

He also knew exactly who she was, before she even knew _what _he was. In one glance at her face, the Intel from his last download provided him with the latest updates to her CIA files in a flash of encoded still images and video clips.

Sarah Walker was her name. Or at least that was her newest cover name. She was a deep undercover operative with an impressive record, he could tell, in spite of him being unable to see much of the information because it had been blacked out on her records due to her high security clearance. Nothing in the flash indicated the reasons why she'd been assigned to watch him. He wasn't surprised on that count. It was fortunate that he'd got as much as he had, if she was as deep as he believed her to be. The question was whether she was assigned to just observe him or if she needed to make contact, as well.

He knew that he should report this sighting to his so-called superiors – he still couldn't quite resist the urge to grimace at the term, as though they were better than him by any stretch of the imagination – but he was very curious to see what she would do next.

Once he had passed Agent Walker, he let out the breath he had been unconsciously holding, and walked as calmly as he could to the Buy More, wondering if the onset of tightness in his chest and stomach could be attributed to nervousness, fear, or excitement.

It wasn't very long before he had his answer about Sarah Walker's mission. He was standing at the Nerd Herder desk with Morgan, on hold on the phone, when she walked into the store and made her way to them.

"Stop the presses," Morgan said lowly, his voice filled with awe. "Is that Vicky Vale?"

Chuck was distracted in the middle of chanting a "Vicky Vale" tune, when he saw her from the corner of his eye and glanced up at her. His heart skipped a beat as he did a double take, then unceremoniously dropped the phone. His following graceless behavior was unfeigned, of course, hopefully giving her the impression that he was just being such a dork because he was a socially inept nerd meeting a beautiful woman out of his league, rather than him knowing who she was and what she most likely wanted.

"I hope I'm not interrupting..." she commented, appearing genuinely amused.

Chuck felt the fight or flight response rising up within him as his initial flustered feelings from being startled turned to real fear. He sensed that the next few minutes of his life were going to change it and he knew that even if he deceived her flawlessly, the end result would mostly likely make him dead. He struggled to maintain control over his responses.

"Nooo. Not at all," he drew out, looking over at Morgan. Somehow, seeing his best friend there and knowing that Morgan's life could depend on the outcome of this meeting, enabled him to reign himself in enough to relax a little. "That's...that's from Batman."

"Cause that makes it better."

"Ha." He wondered if he could sound any more stupid.

"Hi, I'm Morgan," Morgan graciously introduced himself, allowing Chuck a little more time to pull himself together. "And this... This is Chuck."

"Wow, I didn't think anybody named their kids Chuck, anymore. Or Morgan, for that matter," she commented, her manner of speaking flirtatious enough to take any possible sting out of her words.

The line was so well rehearsed and oft used that Chuck couldn't help but respond with it without thinking. "Well, my parents were sadists."

He was surprised at how casually he was able to interact with her after he got over the initial shock and the fear for his life subsided. She really wasn't doing anything other than lose herself almost perfectly in the role of a regular girl – a gorgeous one, but a regular girl, nonetheless -- flirting with a regular, nerdy guy.

He could almost forget that she could throw knives with incredible precision and kill a person with her bare hands in at least a dozen effective ways.

"And he was found in a dumpster by circus freaks." Chuck continued, really getting into this, instinctively knowing that he_ had_ her right where he needed her, which allowed him to consider that this entire situation might not turn out so disastrously as he thought, if he could keep this up.

He missed Morgan's addition, but when he saw the downtrodden face his friend made, it put him right back on track.

"How can I help you..." He very nearly said her name, but managed to avoid it in the nick of time. The near slip was a jarring reminder him that he still needed to stay on his guard. If he spooked her – ha, ha... spooked... lame joke -- then he could well consider his life over before he could really start living it.

"Sarah," she supplied.

"Sarah."

"I'm here about this," she said, pushing her phone to him.

Yes, the IntelCell. It was an easy enough cell phone to feign a problem with. Any Internet search could tell her what kind of problems often came up with that particular model. It would give her sufficient enough of a reason for her to make initial contact without having too much contact.

"Oh yeah, the IntelCell. Yeah, absolutely. This model has a little screw that pops loose right in the back here," he said, in his element now, though he was fixing the phone while they were both playing a dangerous game, deceiving one another. "You just go ahead and give it a few quick turns and good as new. No problem."

"Wow," Sarah said as he handed her phone back. "You geeks are good."

Chuck exchanged a look with Morgan before then they dove right in to a stilted explanation about their preference for the word "nerd" over "geek"

Before Agent Walker could say a word in response, a panicked father approached the Nerd Herder Desk with his tutu costumed daughter. Irritated at the intrusion, yet almost grateful for it, Chuck was caught between wanting to dismiss the man and wanting to help him.

He glanced over at Walker and it looked like she was interested to see how he handled the situation. His decision was made, then. Not only would he be helping a father escape the doghouse his wife would surely put him in for his mistake, but he could make an even better impression on Walker. If she could like him, then maybe she could also spare his life.

He hated how deceptive and manipulative he was capable of being, but this wasn't just his life he was trying to save, but the lives of all the people he cared most deeply about. The sound of his sister's screams still gave him nightmares. He would give anything to keep her from being further traumatized... or killed. They had depended on each other for so long. Captain Awesome remained an incredible help to her as she, even now, continued to come to terms with her terrible experience and move on, thank God, but he had no idea what they were truly up against. And would not be able to help beyond the emotional support his love provided.

Using the wall filled with television screens, they taped the little girl dancing, so they could give it to her mother to watch. Every once in a while, he glanced over at Walker. She was smiling gently and he knew that he had genuinely impressed her. When the taping was finished, Chuck started over to her, only to be accosted by Harry Tang.

He was disappointed when Harry finally moved out of the way and she was gone.

But he knew that he was going to see her again. The ball was in her court now.

When he approached the Nerd Herd desk, Morgan picked something up.

"Dude! She left you a card. Nice."

Chuck smiled awkwardly. First contact had been made and the game was ready to begin. He partially relieved that things had finally been set in motion and partially scared to death that his world was about to crumble and burn.

~*~

As I was writing this, I was appalled that I was actually going to start it off by basically retelling the entire pilot episode. But I now kind of like adding my own little twists to the story.


End file.
